Genome-Wide Association Study Identifies Novel Candidate Genes for Aggressiveness, Deoxynivalenol Production, and Azole Sensitivity in Natural Field Populations of Fusarium graminearum.

Genome-wide association studies can identify novel genomic regions and genes that affect quantitative traits. Fusarium head blight is a destructive disease caused by Fusarium graminearum that exhibits several quantitative traits, including aggressiveness, mycotoxin production, and fungicide resistance. Restriction site-associated DNA sequencing was performed for 220 isolates of F. graminearum. A total of 119 isolates were phenotyped for aggressiveness and deoxynivalenol (DON) production under natural field conditions across four environments. The effective concentration of propiconazole that inhibits isolate growth in vitro by 50% was calculated for 220 strains. Approximately 29,000 single nucleotide polymorphism markers were associated to each trait, resulting in 50, 29, and 74 quantitative trait nucleotides (QTNs) that were significantly associated to aggressiveness, DON production, and propiconazole sensitivity, respectively. Approximately 41% of these QTNs caused nonsynonymous substitutions in predicted exons, while the remainder were synonymous substitutions or located in intergenic regions. Three QTNs associated with propiconazole sensitivity were significant after Bonferroni correction. These QTNs were located in genes not previously associated with azole sensitivity. The majority of the detected QTNs were located in genes with predicted regulatory functions, suggesting that nucleotide variation in regulatory genes plays a major role in the corresponding quantitative trait variation.

Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination.

BACKGROUND: Fusarium graminearum (Fg) is a ubiquitous pathogen of wheat, barley and maize causing Fusarium head blight. Large annual yield losses and contamination of foodstuffs with harmful mycotoxins make Fg one of the most-studied plant pathogens. Analyses of natural field populations can lead to a better understanding of the evolutionary processes affecting this pathogen. Restriction site associated DNA sequencing (RADseq) was used to conduct population genomics analyses including 213 pathogen isolates from 13 German field populations of Fg. RESULTS: High genetic diversity was found within Fg field populations and low differentiation (FST = 0.003) was found among populations. Linkage disequilibrium (LD) decayed rapidly over a distance of 1000 bp. The low multilocus LD indicates that significant sexual recombination occurs in all populations. Several recombination hotspots were detected on each chromosome, but different chromosomes showed different levels of recombination. There was some evidence for selection hotspots. CONCLUSIONS: The population genomic structure of Fg is consistent with a high degree of sexual recombination that is not equally distributed across the chromosomes. The high gene flow found among these field populations should enable this pathogen to adapt rapidly to changes in its environment, including deployment of resistant cultivars, applications of fungicides and a warming climate.

Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight.

BACKGROUND: Fusarium graminearum sensu stricto (s.s.) is an ubiquitous pathogen of cereals. The economic impact of Fusarium head blight (FHB) is characterized by crop losses and mycotoxin contamination. Our objective was to associate SNP diversity within candidate genes with phenotypic traits. A total of 77 F. graminearum s.s. isolates was tested for severity of fungal infection (= aggressiveness) and deoxynivalenol (DON) production in an inoculated field experiment at two locations in each of two years. For seven genes known to control fungal growth (MetAP1, Erf2) or DON production (TRI1, TRI5, TRI6 TRI10 and TRI14) single nucleotides polymorphic sites (SNPs) were determined and evaluated for the extent of linkage disequilibrium (LD). Associations of SNPs with both phenotypic traits were tested using linear mixed models. RESULTS: Decay of LD was in most instances fast. Two neighboring SNPs in MetAP1 and one SNP in Erf2 were significantly (P < 0.05) associated with aggressiveness explaining proportions of genotypic variance (pG) of 25.6%, 0.5%, and 13.1%, respectively. One SNP in TRI1 was significantly associated with DON production (pG = 4.4). CONCLUSIONS: We argue that using the published sequence information of Fusarium graminearum as a template to amplify comparative sequence parts of candidate genes is an effective method to detect quantitative trait loci. Our findings underline the potential of candidate gene association mapping approaches to identify functional SNPs underlying aggressiveness and DON production for F. graminearum s.s populations.

Within-field variation of Fusarium graminearum isolates for aggressiveness and deoxynivalenol production in wheat head blight.

Fusarium head blight (FHB), caused by Fusarium graminearum sensu stricto (s.s.), causes tremendous annual yield losses in wheat worldwide. Variation of aggressiveness of isolates from individual field populations in terms of FHB infection and deoxynivalenol (DON) concentration in the host are important population parameters reflecting parasitic ability. Our main objective was to estimate the variation of both traits within three populations of F. graminearum s.s., each consisting of 30 single-spore isolates collected from small wheat fields in Germany, and to compare it with 11 isolates of a collection (F. graminearum collection) from four countries. The same isolates were characterized using 19 single-sequence repeat markers. All isolates were spray inoculated on a moderately resistant spring wheat cultivar at two field locations over 2 years (i.e., in four environments). The genotypic proportion of phenotypic variance (σ(2)(G)) within populations was significant (P < 0.01) for both traits, and the σ(2)(G) × environment interaction was even more important for mean FHB severity. Ranges in mean FHB severity and DON concentration in the host were only slightly smaller for the field populations than for the F. graminearum collection. Both traits were significantly (P < 0.05) correlated within and across populations. A further partitioning of σ(2)(G) revealed 72% of σ(2)(G) within and 28% of σ(2)(G) across populations for both traits. Molecular variance of the three populations was similarly distributed (73.6% within versus 26.4% between populations). In view of this high within-field variation for traits of parasitic ability and selection, neutral molecular markers, multiple resistance genes of different origin should be employed in wheat breeding programs to obtain a long-term stable FHB resistance.